Aptamers are nucleic acids or peptide molecules that bind targets with an affinity and specificity that rival antibody-antigen interactions. DNA/RNA aptamers promise to provide a cost-effective alternative to antibodies because there is no need for selection in animals or cell lines, they have shelf-lives of years, and they can be easily modified to reduce cross-reactivity with undesired targets. This ability to bind, and in some instances, alter their targets' functions have earned aptamers potential applications in biosensor development, affinity chromatography and recently therapeutics and diagnostics.
Traditionally, artificial aptamer sequences are discovered by SELEX (Systematic Evolution of Ligands by EXponential Enrichment) and other closely related methods of in vitro evolution. Starting libraries have relatively long oligomers of DNA/RNA sequences (80-120 nt) with central randomized regions (30-120 nt). These are sparsely represented libraries with a probability of ˜10−4 that any particular sequence occurs in a typical starting pool for a randomized 30 mer, and of ˜10−29 with randomized 70 mers. This means that nearly all SELEX experiments begin with single copies of those sequences that are present by random chance. Evolution occurs via the selective pressure of binding to a target followed by amplification of the survivors; selection and amplification are repeated in typically 5-20 rounds. Winning aptamers are found by cloning and sequencing, after which a minimal core binding sequence is sought by truncating segments of the parent aptamer that are not needed for the interaction with the target.
Despite the wide adoption of the SELEX procedure for their discovery, DNA/RNA aptamers for only a few hundred targets have been discovered to date using this method compared with the discovery of thousands of antibodies during the same period. This limited success may stem primarily from a significant number of drawbacks with the SELEX method itself. Particularly relevant here, the SELEX methodology of repeated rounds of selection and amplification are cumbersome, time-consuming and very expensive. There is a need for faster and less expensive methods of aptamer discovery and improvement.